[R] About nls.
PIKAL Petr
petr.pikal at precheza.cz
Mon Aug 3 15:04:42 CEST 2015
Hi
Please keep conversation on list somebody can have better idea. Other see in line.
> -----Original Message-----
> From: Jianling Fan [mailto:fanjianling at gmail.com]
> Sent: Friday, July 31, 2015 4:46 PM
> To: PIKAL Petr
> Subject: Re: [R] About nls.
>
> Hello, Petr,
>
> Thanks for your help.
> That works but it change my model. And I think that's not the main
> problem.
> from my data, (den1/R1+den2+den3+den4+den5/R5) always <1, which makes
> (1/(den1/R1+den2+den3+den4+den5/R5)-1)>0.
It is not true unless I have different data from yours.
> with(dat,(den1/0.9+den2+den3+den4+den5/23))
[1] 0.4655556 0.7472222 0.9755556 1.0733333 1.1100000 0.3800000
[7] 0.4800000 0.8500000 0.8800000 1.0000000 0.4800000 0.8900000
[13] 0.9800000 0.9900000 1.0000000 0.2000000 0.3900000 0.6900000
[19] 0.9900000 1.0000000 6.0652174 9.9065217 13.3434783 16.5782609
[25] 18.8021739 19.8130435
> with(dat,(1/(den1/.9+den2+den3+den4+den5/23)-1)>0)
[1] TRUE TRUE TRUE FALSE FALSE TRUE TRUE TRUE TRUE FALSE TRUE TRUE
[13] TRUE TRUE FALSE TRUE TRUE TRUE TRUE FALSE FALSE FALSE FALSE FALSE
[25] FALSE FALSE
>
> str(dat)
'data.frame': 26 obs. of 7 variables:
$ Depth: int 20 40 60 80 100 15 30 45 60 120 ...
$ lnd : num 3 3.69 4.09 4.38 4.61 ...
$ den1 : num 0.419 0.672 0.878 0.966 0.999 ...
$ den2 : num 0 0 0 0 0 0.38 0.48 0.85 0.88 1 ...
$ den3 : num 0 0 0 0 0 0 0 0 0 0 ...
$ den4 : num 0 0 0 0 0 0 0 0 0 0 ...
$ den5 : num 0 0 0 0 0 0 0 0 0 0 ...
>
> dput(dat)
structure(list(Depth = c(20L, 40L, 60L, 80L, 100L, 15L, 30L,
45L, 60L, 120L, 15L, 30L, 45L, 60L, 120L, 15L, 30L, 45L, 60L,
120L, 10L, 30L, 50L, 70L, 90L, 110L), lnd = c(2.995732, 3.688879,
4.094345, 4.382027, 4.60517, 2.70805, 3.401197, 3.806662, 4.094345,
4.787492, 2.70805, 3.401197, 3.806662, 4.094345, 4.787492, 2.70805,
3.401197, 3.806662, 4.094345, 4.787492, 2.302585, 3.401197, 3.912023,
4.248495, 4.49981, 4.70048), den1 = c(0.419, 0.6725, 0.878, 0.966,
0.999, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0), den2 = c(0, 0, 0, 0, 0, 0.38, 0.48, 0.85, 0.88, 1,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0), den3 = c(0,
0, 0, 0, 0, 0, 0, 0, 0, 0, 0.48, 0.89, 0.98, 0.99, 1, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0, 0), den4 = c(0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 0, 0, 0.2, 0.39, 0.69, 0.99, 1, 0, 0, 0, 0, 0, 0),
den5 = c(0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0, 0,
0, 0, 0, 0, 139.5, 227.85, 306.9, 381.3, 432.45, 455.7)), .Names = c("Depth",
"lnd", "den1", "den2", "den3", "den4", "den5"), class = "data.frame", row.names = c("1",
"2", "3", "4", "5", "6", "7", "8", "9", "10", "11", "12", "13",
"14", "15", "16", "17", "18", "19", "20", "21", "22", "23", "24",
"25", "26"))
>
You can check if this is the same as you have. That is why it is preferable to use dput for sending data.
Cheers
Petr
> So, the nls should work in this case. But I don't know why it does not.
>
> Thanks!
>
> Regards,
>
> Julian
>
>
>
> On 31 July 2015 at 00:54, PIKAL Petr <petr.pikal at precheza.cz> wrote:
> > Hi
> >
> > I am not an expert but the problem seems to me that
> >
> > (den1/R1+den2+den3+den4+den5/R5)-1
> >
> > gives you sometimes value 0 and sometimes negative. In these cases
> the value of log(1/result) is NA or Inf and nls can not handle this.
> >
> > I do not search vhere is nls2 from so I used nls and removed -1 form
> your formula, which resulted to some final values.
> >
> >> fit1<-nls(lnd~log(1/(den1/R1+den2+den3+den4+den5/R5))/c+log(d50),
> > + start=c(R1=0.9, R5=23, c=-1.1, d50=10), data=test)
> >>
> >> coef(fit)
> > A B
> > 6.9720965 -0.0272203
> >> coef(fit1)
> > R1 R5 c d50
> > 0.9622249 416.1272498 -0.7178156 73.6017161
> >>
> > Cheers
> > Petr
> >
> >> -----Original Message-----
> >> From: R-help [mailto:r-help-bounces at r-project.org] On Behalf Of
> >> Jianling Fan
> >> Sent: Thursday, July 30, 2015 9:51 PM
> >> To: r-help at r-project.org
> >> Subject: [R] About nls.
> >>
> >> Hello,
> >>
> >> I am trying to do a nls regression with R. but I always get a error
> >> as "Error in numericDeriv(form[[3L]], names(ind), env) : Missing
> >> value or an infinity produced when evaluating the model". I googled
> >> it and found someone said it is because of the improper start value.
> >> I tried many times but can not solve it. Does anyone can help me?
> >>
> >> thanks a lot !
> >>
> >> my code is:
> >>
> >> fit1<-nls2(lnd~log(1/(den1/R1+den2+den3+den4+den5/R5)-1)/c+log(d50),
> >> start=c(R1=0.9, R5=23, c=-1.1, d50=10), data=SWrt)
> >>
> >> data (SWrt) is:
> >>
> >> Depth lnd den1 den2 den3 den4 den5
> >> 1 20 2.995732 0.4190 0.00 0.00 0.00 0.00
> >> 2 40 3.688879 0.6725 0.00 0.00 0.00 0.00
> >> 3 60 4.094345 0.8780 0.00 0.00 0.00 0.00
> >> 4 80 4.382027 0.9660 0.00 0.00 0.00 0.00
> >> 5 100 4.605170 0.9990 0.00 0.00 0.00 0.00
> >> 6 15 2.708050 0.0000 0.38 0.00 0.00 0.00
> >> 7 30 3.401197 0.0000 0.48 0.00 0.00 0.00
> >> 8 45 3.806662 0.0000 0.85 0.00 0.00 0.00
> >> 9 60 4.094345 0.0000 0.88 0.00 0.00 0.00
> >> 10 120 4.787492 0.0000 1.00 0.00 0.00 0.00
> >> 11 15 2.708050 0.0000 0.00 0.48 0.00 0.00
> >> 12 30 3.401197 0.0000 0.00 0.89 0.00 0.00
> >> 13 45 3.806662 0.0000 0.00 0.98 0.00 0.00
> >> 14 60 4.094345 0.0000 0.00 0.99 0.00 0.00
> >> 15 120 4.787492 0.0000 0.00 1.00 0.00 0.00
> >> 16 15 2.708050 0.0000 0.00 0.00 0.20 0.00
> >> 17 30 3.401197 0.0000 0.00 0.00 0.39 0.00
> >> 18 45 3.806662 0.0000 0.00 0.00 0.69 0.00
> >> 19 60 4.094345 0.0000 0.00 0.00 0.99 0.00
> >> 20 120 4.787492 0.0000 0.00 0.00 1.00 0.00
> >> 21 10 2.302585 0.0000 0.00 0.00 0.00 139.50
> >> 22 30 3.401197 0.0000 0.00 0.00 0.00 227.85
> >> 23 50 3.912023 0.0000 0.00 0.00 0.00 306.90
> >> 24 70 4.248495 0.0000 0.00 0.00 0.00 381.30
> >> 25 90 4.499810 0.0000 0.00 0.00 0.00 432.45
> >> 26 110 4.700480 0.0000 0.00 0.00 0.00 455.70
> >>
> >> ______________________________________________
> >> R-help at r-project.org mailing list -- To UNSUBSCRIBE and more, see
> >> https://stat.ethz.ch/mailman/listinfo/r-help
> >> PLEASE do read the posting guide http://www.R-project.org/posting-
> >> guide.html and provide commented, minimal, self-contained,
> >> reproducible code.
> >
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